biology/libsbml: Update to 5.20.0

- Update MASTER_SITES - Update WWW - Sort PLIST Changes: https://github.com/sbmlteam/libsbml/releases
freebsd · May 27, 2023 · f98de8b · f98de8b
1 parent 65881ff
commit f98de8b
Show file tree

Hide file tree

Showing 5 changed files with 199 additions and 566 deletions.
diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile
@@ -1,9 +1,7 @@
 PORTNAME=	libsbml
-PORTVERSION=	5.19.0
-PORTREVISION=	2
+PORTVERSION=	5.20.0
+DISTVERSIONPREFIX=	v
 CATEGORIES=	biology devel
-MASTER_SITES=	SF/sbml/libsbml/${PORTVERSION}/stable
-DISTNAME=	libSBML-${PORTVERSION}-core-src
 
 MAINTAINER=	sunpoet@FreeBSD.org
 COMMENT=	API Library for Working with SBML File
@@ -14,30 +12,54 @@ WWW=		https://sbml.org/software/libsbml/ \
 LICENSE=	LGPL21
 LICENSE_FILE=	${WRKSRC}/COPYING.txt
 
-USES=		cmake iconv:build pathfix
+USES=		cmake:testing iconv:build pathfix
 
-CMAKE_OFF=	EXIT_ON_ERROR LIBSBML_USE_STRICT_INCLUDES PYTHON_USE_API2_WARNINGS WITH_ALL_PACKAGES WITH_CHECK WITH_CPP_NAMESPACE WITH_CSHARP WITH_DOXYGEN WITH_JAVA WITH_JAVASCRIPT WITH_MATLAB WITH_OCTAVE WITH_PERL WITH_PHP WITH_R WITH_STABLE_PACKAGES WITH_WALL
-CMAKE_ON=	LIBSBML_SHARED_VERSION WITH_BZIP2 WITH_SWIG WITH_ZLIB
+CMAKE_OFF=	EXIT_ON_ERROR \
+		LIBSBML_USE_STRICT_INCLUDES \
+		PYTHON_USE_API2_WARNINGS \
+		WITH_ALL_PACKAGES \
+		WITH_CHECK \
+		WITH_CPP_NAMESPACE \
+		WITH_CSHARP \
+		WITH_DOXYGEN \
+		WITH_JAVA \
+		WITH_JAVASCRIPT \
+		WITH_MATLAB \
+		WITH_OCTAVE \
+		WITH_PERL \
+		WITH_PHP \
+		WITH_R \
+		WITH_STABLE_PACKAGES \
+		WITH_WALL
+CMAKE_ON=	LIBSBML_SHARED_VERSION \
+		WITH_BZIP2 \
+		WITH_SWIG \
+		WITH_THREADSAFE_PARSER \
+		WITH_ZLIB
+CMAKE_TESTING_ON=	WITH_CHECK
 USE_CXXSTD=	c++98
 USE_LDCONFIG=	yes
-WRKSRC=		${WRKDIR}/libsbml-${PORTVERSION}
 
 PLIST_SUB=	PORTVERSION=${PORTVERSION}
 
+USE_GITHUB=	yes
+GH_ACCOUNT=	sbmlteam
+
 OPTIONS_DEFINE=	EXAMPLES PYTHON RUBY
 OPTIONS_SINGLE=	XML
 OPTIONS_SINGLE_XML=	EXPAT LIBXML2 XERCES
 OPTIONS_DEFAULT=LIBXML2 PYTHON
 OPTIONS_SUB=	yes
 
+EXAMPLES_CMAKE_BOOL=	WITH_EXAMPLES
 EXPAT_CMAKE_BOOL=	WITH_EXPAT
 EXPAT_LIB_DEPENDS=	libexpat.so:textproc/expat2
 LIBXML2_CMAKE_BOOL=	WITH_LIBXML
 LIBXML2_USE=		GNOME=libxml2
 LIBXML2_USES=		gnome
 PYTHON_BUILD_DEPENDS=	swig:devel/swig
 PYTHON_CMAKE_BOOL=	WITH_PYTHON
-PYTHON_USES=		python:3.6+
+PYTHON_USES=		python:3.7+
 PYTHON_CMAKE_ON=	WITH_SWIG
 RUBY_BUILD_DEPENDS=	swig:devel/swig
 RUBY_CMAKE_BOOL=	WITH_RUBY
@@ -49,7 +71,7 @@ post-patch:
 	@${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|g' ${WRKSRC}/CMakeLists.txt
 
 post-install-EXAMPLES-on:
-	${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
-	cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} '! -name *Makefile*'
+	${MV} ${STAGEDIR}${DATADIR}/examples ${STAGEDIR}${EXAMPLESDIR}
+	${RMDIR} ${STAGEDIR}${DATADIR}
 
 .include <bsd.port.mk>
diff --git a/biology/libsbml/distinfo b/biology/libsbml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1607539653
-SHA256 (libSBML-5.19.0-core-src.tar.gz) = 9d2837378e77a8732588d481327bb10c721ec06dd6cd72f8041d67d3b53d4e56
-SIZE (libSBML-5.19.0-core-src.tar.gz) = 14600103
+TIMESTAMP = 1684104306
+SHA256 (sbmlteam-libsbml-v5.20.0_GH0.tar.gz) = 400f1e1039ef0fc9addc99660a3a2559fefe9cb2c8315b1b488014b6101c438f
+SIZE (sbmlteam-libsbml-v5.20.0_GH0.tar.gz) = 28776286
diff --git a/biology/libsbml/files/patch-CMakeLists.txt b/biology/libsbml/files/patch-CMakeLists.txt
@@ -1,9 +1,56 @@
---- CMakeLists.txt.orig	2020-11-19 11:17:49 UTC
+--- CMakeLists.txt.orig	2023-04-03 10:48:28 UTC
 +++ CMakeLists.txt
-@@ -1297,22 +1297,6 @@ endif()
+@@ -430,8 +430,6 @@ if(WITH_EXPAT)
+     set(LIBSBML_XML_LIBRARY_INCLUDE ${EXPAT_INCLUDE_DIR})
+     set(LIBSBML_XML_LIBRARY_LIBS ${EXPAT_LIBRARY})
+
+-    list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindEXPAT.cmake")
+-
+ endif(WITH_EXPAT)
+
+
+@@ -452,8 +450,6 @@ if(WITH_LIBXML)
+   set(LIBSBML_XML_LIBRARY_INCLUDE ${LIBXML_INCLUDE_DIR})
+   set(LIBSBML_XML_LIBRARY_LIBS ${LIBXML_LIBRARY})
+
+-  list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindLIBXML.cmake")
+-
+ endif(WITH_LIBXML)
+
+
+@@ -473,8 +469,6 @@ if(WITH_XERCES)
+     set(LIBSBML_XML_LIBRARY_INCLUDE ${XERCES_INCLUDE_DIR})
+     set(LIBSBML_XML_LIBRARY_LIBS ${XERCES_LIBRARY})
+
+-    list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindXERCES.cmake")
+-
+ endif(WITH_XERCES)
 
  ###############################################################################
- #
+@@ -498,7 +492,6 @@ if(WITH_BZIP2)
+   set(USE_BZ2 ON)
+   add_definitions( -DUSE_BZ2 )
+   list(APPEND SWIG_EXTRA_ARGS -DUSE_BZ2)
+-  list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindBZ2.cmake")
+ endif(WITH_BZIP2)
+
+
+@@ -608,8 +601,6 @@ valid. It should contain the file zlib.h, but it does 
+       INTERFACE_INCLUDE_DIRECTORIES "${LIBZ_INCLUDE_DIR}")
+   endif()
+
+-  list(APPEND LIBSBML_FIND_MODULES "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/FindZLIB.cmake")
+-
+ endif(WITH_ZLIB)
+
+ # install find scripts only for used dependencies
+@@ -981,22 +972,6 @@ if(WITH_DOXYGEN)
+     add_subdirectory(docs)
+ endif()
+
+-
+-###############################################################################
+-#
 -# Install documentation
 -#
 -
@@ -17,9 +64,6 @@
 -)
 -
 -install(FILES ${DOCUMENTATION_FILES} DESTINATION ${MISC_PREFIX})
--
--###############################################################################
--#
- # Write libsbml.pc
- #
 
+ ###############################################################################
+ #